The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
Quantitative Modelling Explains Distinct STAT1 and STAT3
bioRxiv preprint doi: https://doi.org/10.1101/425868; this version posted September 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Title Quantitative modelling explains distinct STAT1 and STAT3 activation dynamics in response to both IFNγ and IL-10 stimuli and predicts emergence of reciprocal signalling at the level of single cells. 1,2, 3 1 1 1 1 1 2 Sarma U , Maitreye M , Bhadange S , Nair A , Srivastava A , Saha B , Mukherjee D . 1: National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, India. 2 : Corresponding author. [email protected] , [email protected] 3: Present address. Labs, Persistent Systems Limited, Pingala – Aryabhata, Erandwane, Pune, 411004 India. bioRxiv preprint doi: https://doi.org/10.1101/425868; this version posted September 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Cells use IFNγ-STAT1 and IL-10-STAT3 pathways primarily to elicit pro and anti-inflammatory responses, respectively. However, activation of STAT1 by IL-10 and STAT3 by IFNγ is also observed. The regulatory mechanisms controlling the amplitude and dynamics of both the STATs in response to these functionally opposing stimuli remains less understood. Here, our experiments at cell population level show distinct early signalling dynamics of both STAT1 and STAT3(S/1/3) in responses to IFNγ and IL-10 stimulation. -
IRF8 Regulates Gram-Negative Bacteria–Mediated NLRP3 Inflammasome Activation and Cell Death
IRF8 Regulates Gram-Negative Bacteria− Mediated NLRP3 Inflammasome Activation and Cell Death This information is current as Rajendra Karki, Ein Lee, Bhesh R. Sharma, Balaji Banoth of September 25, 2021. and Thirumala-Devi Kanneganti J Immunol published online 23 March 2020 http://www.jimmunol.org/content/early/2020/03/20/jimmun ol.1901508 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2020/03/20/jimmunol.190150 Material 8.DCSupplemental http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 25, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2020 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published March 23, 2020, doi:10.4049/jimmunol.1901508 The Journal of Immunology IRF8 Regulates Gram-Negative Bacteria–Mediated NLRP3 Inflammasome Activation and Cell Death Rajendra Karki,*,1 Ein Lee,*,†,1 Bhesh R. Sharma,*,1 Balaji Banoth,* and Thirumala-Devi Kanneganti* Inflammasomes are intracellular signaling complexes that are assembled in response to a variety of pathogenic or physiologic stimuli to initiate inflammatory responses. -
Reduced Expression of IL-12 Receptor B2 and IL-18 Receptor a Genes in Natural Killer Cells and Macrophages Derived from B6-Mi/Mi Mice
Laboratory Investigation (2005) 85, 146–153 & 2005 USCAP, Inc All rights reserved 0023-6837/05 $30.00 www.laboratoryinvestigation.org Reduced expression of IL-12 receptor b2 and IL-18 receptor a genes in natural killer cells and macrophages derived from B6-mi/mi mice Tatsuki R Kataoka1,2, Nobuyasu Komazawa3, Keisuke Oboki1, Eiichi Morii1 and Toru Nakano1,4 1Department of Pathology, Medical School/Graduate School of Frontier Bioscience, Osaka University, Osaka, Japan; 2Department of Pathology, Osaka Medical Center for Cancer and Cardiovascular Disease, Osaka, Japan; 3Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan and 4Department of Molecular Cell Biology, Research Institute for Microbial Disease, Osaka University, Osaka, Japan The mi transcriptional factor (MITF) is a basic helix–loop–helix leucine zipper-type transcriptional factor. The mi mutant allele encodes an abnormal MITF, in which one out of four consecutive arginines is deleted in the basic domain. The VGA-9-tg (tg) allele is another mutant allele and considered to be a null mutant allele. C57BL/6 (B6)- mi/mi mice showed abnormal phenotypes of natural killer (NK) cells and macrophages, whereas B6-tg/tg mice did not. The expression levels of the genes for the interleukin-12 receptor (IL-12R) b2 and IL-18Ra were reduced in both the NK cells and macrophages of B6-mi/mi mice, while the expression levels of the corresponding genes in B6-tg/tg mice were unaffected. The B6-mi/mi NK cells and B6-mi/mi macrophages showed impaired responses to stimulation with IL-12, IL-18, and IL-12 plus IL-18 stimulation. -
PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain
Published OnlineFirst April 26, 2017; DOI: 10.1158/2159-8290.CD-16-1297 RESEARCH ARTICLE PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability Berkley E. Gryder 1 , Marielle E. Yohe 1 , 2 , Hsien-Chao Chou 1 , Xiaohu Zhang 3 , Joana Marques 4 , Marco Wachtel4 , Beat Schaefer 4 , Nirmalya Sen 1 , Young Song 1 , Alberto Gualtieri 5 , Silvia Pomella 5 , Rossella Rota5 , Abigail Cleveland 1 , Xinyu Wen 1 , Sivasish Sindiri 1 , Jun S. Wei 1 , Frederic G. Barr 6 , Sudipto Das7 , Thorkell Andresson 7 , Rajarshi Guha 3 , Madhu Lal-Nag 3 , Marc Ferrer 3 , Jack F. Shern 1 , 2 , Keji Zhao8 , Craig J. Thomas 3 , and Javed Khan 1 Downloaded from cancerdiscovery.aacrjournals.org on September 29, 2021. © 2017 American Association for Cancer Research. 16-CD-16-1297_p884-899.indd 884 7/20/17 2:21 PM Published OnlineFirst April 26, 2017; DOI: 10.1158/2159-8290.CD-16-1297 ABSTRACT Alveolar rhabdomyosarcoma is a life-threatening myogenic cancer of children and ado- lescent young adults, driven primarily by the chimeric transcription factor PAX3–FOXO1. The mechanisms by which PAX3–FOXO1 dysregulates chromatin are unknown. We fi nd PAX3–FOXO1 repro- grams the cis -regulatory landscape by inducing de novo super enhancers. PAX3–FOXO1 uses super enhancers to set up autoregulatory loops in collaboration with the master transcription factors MYOG, MYOD, and MYCN. This myogenic super enhancer circuitry is consistent across cell lines and primary tumors. Cells harboring the fusion gene are selectively sensitive to small-molecule inhibition of protein targets induced by, or bound to, PAX3–FOXO1-occupied super enhancers. -
PAX3-FOXO1A Expression in Rhabdomyosarcoma Is Driven by the Targetable Nuclear Receptor NR4A1 Alexandra Lacey1, Aline Rodrigues-Hoffman2, and Stephen Safe1
Published OnlineFirst November 18, 2016; DOI: 10.1158/0008-5472.CAN-16-1546 Cancer Therapeutics, Targets, and Chemical Biology Research PAX3-FOXO1A Expression in Rhabdomyosarcoma Is Driven by the Targetable Nuclear Receptor NR4A1 Alexandra Lacey1, Aline Rodrigues-Hoffman2, and Stephen Safe1 Abstract Alveolar rhabdomyosarcoma (ARMS) is a devastating pediatric PAX3-FOXO1A. Mechanistic investigations revealed a requirement disease driven by expression of the oncogenic fusion gene PAX3- for the NR4A1/Sp4 complex to bind GC-rich promoter regions FOXO1A. In this study, we report overexpression of the nuclear to elevate transcription of the PAX3-FOXO1A gene. In parallel, receptor NR4A1 in rhabdomyosarcomas that is sufficient to NR4A1 also regulated expression of b1-integrin, which with PAX3- drive high expression of PAX3-FOXO1A there. RNAi-mediated FOXO1A, contributed to tumor cell migration that was blocked by silencing of NR4A1 decreased expression of PAX3-FOXO1A and C-DIM/NR4A1 antagonists. Taken together, our results provide a its downstream effector genes. Similarly, cell treatment with the preclinical rationale for the use of NR4A1 small-molecule antago- NR4A1 small-molecule antagonists 1,1-bis(3-indolyl)-1-(p- nists to treat ARMS and other rhabdomyosarcomas driven by hydroxy or p-carbomethoxyphenyl)methane (C-DIM) decreased PAX3-FOXO1A. Cancer Res; 77(3); 1–10. Ó2016 AACR. Introduction activity for NR4A1. In contrast, NR4A1 exhibits tumor promoter activity (6, 7) in solid tumors. NR4A1 is also overexpressed in Rhabdomyosarcoma is the most common soft-tissue sarco- tumors from patients with breast, lung, pancreatic, colon, and ma that is primarily observed in children and adolescents and ovarian cancer and is a negative prognostic factor for patients with accounts for 50% of all pediatric cancers and 50% of soft-tissue breast, lung, and ovarian cancer (9–15). -
STAT1 Signalling Predicts Response to Chemotherapy in Oestrogen Receptor-Negative Breast Cancer
FULL PAPER British Journal of Cancer (2016) 114, 177–187 | doi: 10.1038/bjc.2015.398 Keywords: STAT1; ER-negative breast cancer; IFN; chemotherapy; predictive signature Activation of IFN/STAT1 signalling predicts response to chemotherapy in oestrogen receptor-negative breast cancer Marie-Emmanuelle Legrier1, Ivan Bie` che2, Julie Gaston1, Arnaud Beurdeley1, Vanessa Yvonnet1, Olivier De´as1, Aure´ lie Thuleau3, Sophie Chaˆ teau-Joubert4, Jean-Luc Servely4,5, Sophie Vacher2, Myriam Lassalle1, Ste´ phane Depil6, Gordon C Tucker6, Jean-Jacques Fontaine4, Marie-France Poupon1, Sergio Roman-Roman3, Jean-Gabriel Judde1, Didier Decaudin3,7, Stefano Cairo*,1,8,9 and Elisabetta Marangoni*,3,9 1XenTech, 4 rue Pierre Fontaine, Evry 91000, France; 2Genetics Department, Hospital, Institut Curie, 26 rue d’Ulm, Paris 75005, France; 3Translational Research Department, Institut Curie, 26 rue d’Ulm, Paris 75005, France; 4Department of Pathology, Veterinary School of Alfort, Maisons-Alfort 94704, France; 5INRA, Phase Department, Nouzilly, France; 6Institut de Recherches Servier, PIT Oncology, Croissy-sur-Seine 78290, France; 7Medical Oncology Department, Institut Curie, 26 rue d’Ulm, Paris 75005, France and 8University of Ferrara, LTTA Centre, Department of Morphology, Surgery and Experimental Medicine, Ferrara, Italy Background: Oestrogen receptor-negative (ER À ) breast cancer is intrinsically sensitive to chemotherapy. However, tumour response is often incomplete, and relapse occurs with high frequency. The aim of this work was to analyse the molecular characteristics of residual tumours and early response to chemotherapy in patient-derived xenografts (PDXs) of breast cancer. Methods: Gene and protein expression profiles were analysed in a panel of ER À breast cancer PDXs before and after chemotherapy treatment. -
Estrogen Receptors and Ubiquitin Proteasome System: Mutual Regulation
biomolecules Review Estrogen Receptors and Ubiquitin Proteasome System: Mutual Regulation Irina V. Kondakova 1 , Elena E. Shashova 1, Evgenia A. Sidenko 1, Tatiana M. Astakhova 2, Liudmila A. Zakharova 2 and Natalia P. Sharova 2,* 1 Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; [email protected] (I.V.K.); [email protected] (E.E.S.); [email protected] (E.A.S.) 2 Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; [email protected] (T.M.A.); [email protected] (L.A.Z.) * Correspondence: [email protected]; Tel.: +7-499-135-7674; Fax: +7-499-135-3322 Received: 16 February 2020; Accepted: 25 March 2020; Published: 26 March 2020 Abstract: This review provides information on the structure of estrogen receptors (ERs), their localization and functions in mammalian cells. Additionally, the structure of proteasomes and mechanisms of protein ubiquitination and cleavage are described. According to the modern concept, the ubiquitin proteasome system (UPS) is involved in the regulation of the activity of ERs in several ways. First, UPS performs the ubiquitination of ERs with a change in their functional activity. Second, UPS degrades ERs and their transcriptional regulators. Third, UPS affects the expression of ER genes. In addition, the opportunity of the regulation of proteasome functioning by ERs—in particular, the expression of immune proteasomes—is discussed. Understanding the complex mechanisms underlying the regulation of ERs and proteasomes has great prospects for the development of new therapeutic agents that can make a significant contribution to the treatment of diseases associated with the impaired function of these biomolecules. -
PAX3-FOXO1A Expression in Rhabdomyosarcoma Is Driven by the Targetable Nuclear Receptor NR4A1 Alexandra Lacey1, Aline Rodrigues-Hoffman2, and Stephen Safe1
Published OnlineFirst November 18, 2016; DOI: 10.1158/0008-5472.CAN-16-1546 Cancer Therapeutics, Targets, and Chemical Biology Research PAX3-FOXO1A Expression in Rhabdomyosarcoma Is Driven by the Targetable Nuclear Receptor NR4A1 Alexandra Lacey1, Aline Rodrigues-Hoffman2, and Stephen Safe1 Abstract Alveolar rhabdomyosarcoma (ARMS) is a devastating pediatric PAX3-FOXO1A. Mechanistic investigations revealed a requirement disease driven by expression of the oncogenic fusion gene PAX3- for the NR4A1/Sp4 complex to bind GC-rich promoter regions FOXO1A. In this study, we report overexpression of the nuclear to elevate transcription of the PAX3-FOXO1A gene. In parallel, receptor NR4A1 in rhabdomyosarcomas that is sufficient to NR4A1 also regulated expression of b1-integrin, which with PAX3- drive high expression of PAX3-FOXO1A there. RNAi-mediated FOXO1A, contributed to tumor cell migration that was blocked by silencing of NR4A1 decreased expression of PAX3-FOXO1A and C-DIM/NR4A1 antagonists. Taken together, our results provide a its downstream effector genes. Similarly, cell treatment with the preclinical rationale for the use of NR4A1 small-molecule antago- NR4A1 small-molecule antagonists 1,1-bis(3-indolyl)-1-(p- nists to treat ARMS and other rhabdomyosarcomas driven by hydroxy or p-carbomethoxyphenyl)methane (C-DIM) decreased PAX3-FOXO1A. Cancer Res; 77(3); 1–10. Ó2016 AACR. Introduction activity for NR4A1. In contrast, NR4A1 exhibits tumor promoter activity (6, 7) in solid tumors. NR4A1 is also overexpressed in Rhabdomyosarcoma is the most common soft-tissue sarco- tumors from patients with breast, lung, pancreatic, colon, and ma that is primarily observed in children and adolescents and ovarian cancer and is a negative prognostic factor for patients with accounts for 50% of all pediatric cancers and 50% of soft-tissue breast, lung, and ovarian cancer (9–15). -
A Dual Cis-Regulatory Code Links IRF8 to Constitutive and Inducible Gene Expression in Macrophages
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages Alessandra Mancino,1,3 Alberto Termanini,1,3 Iros Barozzi,1 Serena Ghisletti,1 Renato Ostuni,1 Elena Prosperini,1 Keiko Ozato,2 and Gioacchino Natoli1 1Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy; 2Laboratory of Molecular Growth Regulation, Genomics of Differentiation Program, National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA The transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8–PU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRF–AP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome. -
In Mediating Transcriptional Activity of Androgen Receptor Splice Variants
ROLE OF TRANSCRIPTIONAL ACTIVATION UNIT 5 (TAU5) IN MEDIATING TRANSCRIPTIONAL ACTIVITY OF ANDROGEN RECEPTOR SPLICE VARIANTS A THESIS SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY SARITA KUMARI MUTHA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE SCOTT DEHM & JIM McCARTHY DECEMBER 2012 © Sarita Kumari Mutha 2012 ACKNOWLEDGEMENTS I would like to thank the Dehm Lab: Scott Dehm, Yingming Li, Siu Chiu Chan, and Luke Brand for the support, discussions, journal clubs, and training. I would like to thank MCBD&G faculty Kathleen Conklin and Meg Titus for their support. Finally, I would also to acknowledge my committee Scott Dehm, Jim McCarthy, and Kaylee Schwertfeger for their time and support. i DEDICATION This thesis is dedicated to my mentor and advisor Scott Dehm. This work would not have been possible without his support. I am very grateful for my time under his mentorship and the opportunity to learn from him. ii ABSTRACT The standard treatment for advanced prostate cancer is chemical castration, which inhibits the activity of the androgen receptor (AR). Eventually, prostate cancer reemerges with a castration-resistant phenotype (CRPC) but still depends on AR signaling. One mechanism of AR activity in CRPC is the synthesis of AR splice variants, which lack the ligand binding domain. These splice variants function as constitutively active transcription factors that promote expression of endogenous AR target genes and support androgen independent prostate cancer cell growth. Previous work has shown transcriptional activation unit 5 (TAU5) is necessary for ligand independent activity of the full length AR in low or no androgen conditions and that this activation is mediated by the WHTLF motif. -
Modulation of STAT Signaling by STAT-Interacting Proteins
Oncogene (2000) 19, 2638 ± 2644 ã 2000 Macmillan Publishers Ltd All rights reserved 0950 ± 9232/00 $15.00 www.nature.com/onc Modulation of STAT signaling by STAT-interacting proteins K Shuai*,1 1Departments of Medicine and Biological Chemistry, University of California, Los Angeles, California, CA 90095, USA STATs (signal transducer and activator of transcription) play important roles in numerous cellular processes Interaction with non-STAT transcription factors including immune responses, cell growth and dierentia- tion, cell survival and apoptosis, and oncogenesis. In Studies on the promoters of a number of IFN-a- contrast to many other cellular signaling cascades, the induced genes identi®ed a conserved DNA sequence STAT pathway is direct: STATs bind to receptors at the named ISRE (interferon-a stimulated response element) cell surface and translocate into the nucleus where they that mediates IFN-a response (Darnell, 1997; Darnell function as transcription factors to trigger gene activa- et al., 1994). Stat1 and Stat2, the ®rst known members tion. However, STATs do not act alone. A number of of the STAT family, were identi®ed in the transcription proteins are found to be associated with STATs. These complex ISGF-3 (interferon-stimulated gene factor 3) STAT-interacting proteins function to modulate STAT that binds to ISRE (Fu et al., 1990, 1992; Schindler et signaling at various steps and mediate the crosstalk of al., 1992). ISGF-3 consists of a Stat1:Stat2 heterodimer STATs with other cellular signaling pathways. This and a non-STAT protein named p48, a member of the article reviews the roles of STAT-interacting proteins in IRF (interferon regulated factor) family (Levy, 1997).